diff --git a/main.c b/main.c
index c7c152a..56d2afc 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r462-dirty"
+#define MM_VERSION "2.2-r463-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -40,6 +40,7 @@ static struct option long_options[] = {
 	{ "multi",          optional_argument, 0, 0 },
 	{ "no-long-join",   no_argument,       0, 0 },
 	{ "seed",           required_argument, 0, 0 },
+	{ "print-2nd",      optional_argument, 0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -124,6 +125,10 @@ int main(int argc, char *argv[])
 			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
 				opt.flag |= MM_F_MULTI_SEG;
 			else opt.flag &= ~MM_F_MULTI_SEG;
+		} else if (c == 0 && long_idx ==17) { // --print-2nd
+			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
+				opt.flag &= ~MM_F_NO_PRINT_2ND;
+			else opt.flag |= MM_F_NO_PRINT_2ND;
 		} else if (c == 'V') {
 			puts(MM_VERSION);
 			return 0;
diff --git a/map.c b/map.c
index b6ea3d8..3a9e3a0 100644
--- a/map.c
+++ b/map.c
@@ -80,7 +80,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->min_dp_max = 200;
 	} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
 		io->is_hpc = 0, io->k = 21, io->w = 11;
-		mo->flag |= MM_F_SR | MM_F_MULTI_SEG;
+		mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_NO_PRINT_2ND;
 		mo->pe_ori = 0<<1|1; // FR
 		mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
 		mo->max_gap = 200;
@@ -452,6 +452,9 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			mm_bseq1_t *t = &s->seq[i];
 			for (j = 0; j < s->n_reg[i]; ++j) {
 				mm_reg1_t *r = &s->reg[i][j];
+				assert(!r->sam_pri || r->id == r->parent);
+				if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
+					continue;
 				if (p->opt->flag & MM_F_OUT_SAM)
 					mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
 				else
diff --git a/minimap.h b/minimap.h
index ef93024..51a0742 100644
--- a/minimap.h
+++ b/minimap.h
@@ -19,6 +19,7 @@
 #define MM_F_NO_SAM_SQ   0x800
 #define MM_F_SR          0x1000
 #define MM_F_MULTI_SEG   0x2000
+#define MM_F_NO_PRINT_2ND  0x4000
 
 #define MM_IDX_MAGIC   "MMI\2"